for the interactions between the motor and the host atoms.
Our medium is a fragile liquid[1]}, [2]} that falls out of equilibrium in bulk simulations below \(T=340 K\) , i.e. \(T=340\)  K is the smallest temperature for which we can equilibrate the bulk liquid when the motor is not active.
Consequently the bulk medium above that temperature behaves as a viscous supercooled liquid in our simulations while below it behaves as a solid (as \(t_{simulation}<\tau _{\alpha }\) ).
Notice however that when active, the motor's motions induce a fluidization of the medium around it[3]}, [4]}, [5]}, [6]}, [7]}, [8]}, [9]}, [10]}, an effect that has been experimentally demonstrated[4]}, [5]}, [6]}, [7]}, [9]} with azobenzene photo-isomerizing molecules embedded in soft matter, a result that has been linked[16]}, [17]} to the cooperative dynamics[18]} arising at the approach of the glass transition.
We evaluate the glass transition temperature \(T_{g}\)  in the bulk to be slightly smaller \(T_{g} \approx 250 K\) .
Notice that as they are modeled with Lennard-Jones atoms, the host and motor potentials are quite versatile.
Due to that property, a shift in the parameters \(\epsilon \)  will shift all the temperatures by the same amount, including the glass-transition temperature and the melting temperature of the material.
Each folding is modeled as continuous, using a constant quaternion variation, with a folding time \(\tau _{f}=0.3 ps\) .
The total cycle period is constant and fixed at \(\tau _{p}=400 ps\) .
The folded and unfolded part of the cycle have the same duration equal to \(\tau _{p}/2=200 ps\)  including the \(0.3 ps\)  folding or unfolding.
Our system, while out of equilibrium, is in a steady state and is not aging. That behavior is obtained because the energy released by the motor into the medium is small enough and the time lapse between two stimuli large enough for the system to relax before a new stimuli appears.
In other words we are in the linear response regime[19]}.
Through this work we use the mean square displacements of the motor to measure its ability to diffuse.
The mean square displacement is defined as[20]}:
\(\displaystyle {<r^{2}(t)>= {1\over N.N_{t_{0}}} \sum _{i,t_{0}} \mid {{\bf r}_{i}(t+t_{0})-{\bf r}_{i}(t_{0})} }\mid ^{2} \) 
